def getAtomTypeCounts(self, atomNames):
atomNames = atomNames.lstrip('[')
atomNames = atomNames.rstrip(']')
atomNames = atomNames.rstrip()
atomList = atomNames.split(" ") #atom names
peptideAtomCount = 0
proteinAtomCount = 0
for atom in atomList:
[chain, residue, atom] = atomicDominoUtilities.getAtomInfoFromName(atom)
if (chain == self.getParam("peptide_chain")):
peptideAtomCount += 1
else:
proteinAtomCount += 1
return [peptideAtomCount, proteinAtomCount]
def writeCytoscapeIgInput(self):
outputDir = self.getParam("output_directory")
igOutputFile = self.getParam("ig_output_file")
[nodesToNames, nodesToNodes] = self.getGraphStructure(self.ig, os.path.join(outputDir, igOutputFile), "-")
self.writeEdgeFile(nodesToNodes, self.getParam("ig_cytoscape_input_file"))
#write residue numbers for each node
igResiduesFile = self.getParam("ig_cytoscape_residues_file")
peptideChain = self.getParam("peptide_chain")
subsetResidueFile = open(os.path.join(outputDir, igResiduesFile), 'w')
subsetResidueFile.write("ResidueNumber\n")
for nodeNumber in nodesToNames.keys():
nodeName = nodesToNames[nodeNumber]
[nodeChain, residueNumber, nodeAtom] = atomicDominoUtilities.getAtomInfoFromName(nodeName)
if (nodeChain == peptideChain): #peptideAtom
subsetResidueFile.write("%s = %s\n" % (nodeNumber, residueNumber))
else:
subsetResidueFile.write("%s = 100\n" % nodeNumber) #for now just write arbitrary number to designate as protein atom
